X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=bd1400b5eba09f412f17dd415d3810bf79a56ec1;hb=5b3d1cf1e78adbeeedf14eec91b6a0be75ca21e4;hp=0e2b6302df99dcfe3d16e6fbaf0c92b07aa28fb6;hpb=9310ac1d3638a692a43323c4e9ee2d93a658a475;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 0e2b630..bd1400b 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -30,32 +30,43 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; import java.io.File; import java.util.BitSet; import java.util.HashMap; import java.util.Map; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class StockholmFileTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + static String PfamFile = "examples/PF00111_seed.stk", RfamFile = "examples/RF00031_folded.stk"; @Test(groups = { "Functional" }) public void pfamFileIO() throws Exception { - testFileIOwithFormat(new File(PfamFile), "STH", -1, 0); + testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0, + false); } @Test(groups = { "Functional" }) public void pfamFileDataExtraction() throws Exception { AppletFormatAdapter af = new AppletFormatAdapter(); - AlignmentI al = af.readFile(PfamFile, af.FILE, - new IdentifyFile().identify(PfamFile, af.FILE)); + AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE, + new IdentifyFile().identify(PfamFile, DataSourceType.FILE)); int numpdb = 0; for (SequenceI sq : al.getSequences()) { @@ -72,7 +83,8 @@ public class StockholmFileTest @Test(groups = { "Functional" }) public void rfamFileIO() throws Exception { - testFileIOwithFormat(new File(RfamFile), "STH", 2, 1); + testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1, + false); } /** @@ -84,10 +96,11 @@ public class StockholmFileTest * @param ioformat * - label for IO class used to write and read back in the data from * f + * @param ignoreRowVisibility */ - public static void testFileIOwithFormat(File f, String ioformat, - int naliannot, int nminseqann) + public static void testFileIOwithFormat(File f, FileFormatI ioformat, + int naliannot, int nminseqann, boolean ignoreRowVisibility) { System.out.println("Reading file: " + f); String ff = f.getPath(); @@ -95,26 +108,26 @@ public class StockholmFileTest { AppletFormatAdapter rf = new AppletFormatAdapter(); - AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().identify(ff, AppletFormatAdapter.FILE)); + AlignmentI al = rf.readFile(ff, DataSourceType.FILE, + new IdentifyFile().identify(ff, DataSourceType.FILE)); assertNotNull("Couldn't read supplied alignment data.", al); // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); + al.getSequenceAt(i).createDatasetSequence(); } String outputfile = rf.formatSequences(ioformat, al, true); System.out.println("Output file in '" + ioformat + "':\n" + outputfile + "\n< i) { - assertTrue("Different alignment annotation at position " + i, - equalss(aa_original[i], aa_new[i])); + assertEqualSecondaryStructure( + "Different alignment annotation at position " + i, + aa_original[i], aa_new[i]); // compare graphGroup or graph properties - needed to verify JAL-1299 assertEquals("Graph type not identical.", aa_original[i].graph, aa_new[i].graph); - assertEquals("Visibility not identical.", aa_original[i].visible, + if (!ignoreRowVisibility) + { + assertEquals("Visibility not identical.", + aa_original[i].visible, aa_new[i].visible); + } assertEquals("Threshold line not identical.", aa_original[i].threshold, aa_new[i].threshold); // graphGroup may differ, but pattern should be the same @@ -281,8 +320,7 @@ public class StockholmFileTest assertEquals("different number of features", seq_original[i].getSequenceFeatures().length, - seq_new[in] - .getSequenceFeatures().length); + seq_new[in].getSequenceFeatures().length); for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) { @@ -302,8 +340,9 @@ public class StockholmFileTest { annot_original = al.getSequenceAt(i).getAnnotation()[j]; annot_new = al_input.getSequenceAt(in).getAnnotation()[j]; - assertTrue("Different annotation elements", - equalss(annot_original, annot_new)); + assertEqualSecondaryStructure( + "Different annotation elements", annot_original, + annot_new); } } } @@ -325,39 +364,57 @@ public class StockholmFileTest } } - /* - * compare annotations - */ - private static boolean equalss(AlignmentAnnotation annot_or, + private static void assertEqualSecondaryStructure(String message, + AlignmentAnnotation annot_or, AlignmentAnnotation annot_new) { + // TODO: test to cover this assert behaves correctly for all allowed + // variations of secondary structure annotation row equivalence if (annot_or.annotations.length != annot_new.annotations.length) { - System.err.println("Different lengths for annotation row elements: " + fail("Different lengths for annotation row elements: " + annot_or.annotations.length + "!=" + annot_new.annotations.length); - return false; } + boolean isRna = annot_or.isRNA(); + assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ") + + " secondary structure in the row.", + isRna == annot_new.isRNA()); for (int i = 0; i < annot_or.annotations.length; i++) { Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i]; if (an_or != null && an_new != null) { - if (!an_or.displayCharacter.trim().equals( - an_new.displayCharacter.trim()) - || !("" + an_or.secondaryStructure).trim().equals( - ("" + an_new.secondaryStructure).trim()) - || (an_or.description != an_new.description && !((an_or.description == null && an_new.description - .trim().length() == 0) - || (an_new.description == null && an_or.description - .trim().length() == 0) || an_or.description - .trim().equals(an_new.description.trim())))) + + if (isRna) { - System.err.println("Annotation Element Mismatch\nElement " + i - + " in original: " + annot_or.annotations[i].toString() - + "\nElement " + i + " in new: " - + annot_new.annotations[i].toString()); - return false; + if (an_or.secondaryStructure != an_new.secondaryStructure + || an_or.value != an_new.value) + { + fail("Different RNA secondary structure at column " + i + + " expected: [" + annot_or.annotations[i].toString() + + "] but got: [" + annot_new.annotations[i].toString() + + "]"); + } + } + else + { + // not RNA secondary structure, so expect all elements to match... + if (!an_or.displayCharacter.trim().equals( + an_new.displayCharacter.trim()) + || !("" + an_or.secondaryStructure).trim().equals( + ("" + an_new.secondaryStructure).trim()) + || (an_or.description != an_new.description && !((an_or.description == null && an_new.description + .trim().length() == 0) + || (an_new.description == null && an_or.description + .trim().length() == 0) || an_or.description + .trim().equals(an_new.description.trim())))) + { + fail("Annotation Element Mismatch\nElement " + i + + " in original: " + annot_or.annotations[i].toString() + + "\nElement " + i + " in new: " + + annot_new.annotations[i].toString()); + } } } else if (annot_or.annotations[i] == null @@ -367,7 +424,7 @@ public class StockholmFileTest } else { - System.err.println("Annotation Element Mismatch\nElement " + fail("Annotation Element Mismatch\nElement " + i + " in original: " + (annot_or.annotations[i] == null ? "is null" @@ -377,9 +434,53 @@ public class StockholmFileTest + " in new: " + (annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString())); - return false; } } - return true; + } + + String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG"; + String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n" + + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t" + + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t" + + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false"; + + String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n" + + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t" + + "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]\t0.0\nROWPROPERTIES\t" + + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false"; + + @Test(groups = { "Functional" }) + public void secondaryStructureForRNASequence() throws Exception + { + roundTripSSForRNA(aliFile, annFile); + } + + @Test(groups = { "Functional" }) + public void fullWUSSsecondaryStructureForRNASequence() throws Exception + { + roundTripSSForRNA(aliFile, annFileFullWuss); + } + + private static void roundTripSSForRNA(String aliFile, String annFile) + throws Exception + { + AlignmentI al = new AppletFormatAdapter().readFile(aliFile, + DataSourceType.PASTE, jalview.io.FileFormat.Fasta); + AnnotationFile aaf = new AnnotationFile(); + aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE); + al.getAlignmentAnnotation()[0].visible = true; + + // TODO: create a better 'save as ' pattern + StockholmFile sf = new StockholmFile(al); + + String stockholmFile = sf.print(al.getSequencesArray(), true); + + AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile, + DataSourceType.PASTE, jalview.io.FileFormat.Stockholm); + // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport() + // .getAlignment(), Arrays.asList("Secondary Structure"), newAl + // .getViewport().getAlignment().getSequences(), true, true); + testAlignmentEquivalence(al, newAl, true, true); + } }